Ewan Birney

NAME

Bio::DB::Biblio::biofetch - A BioFetch-based access to a bibliographic citation retrieval

SYNOPSIS

Do not use this object directly, only access it through the Bio::Biblio module:

  use Bio::Biblio;
  my $biblio = new Bio::Biblio (-access => 'biofetch');
  my $ref = $biblio->get_by_id('20063307'));

  my $ids = ['20063307', '98276153'];
  my $refio = $biblio->get_all($ids);
  while ($ref = $refio->next_bibref) { 
    print $ref->identifier, "\n";
  }

DESCRIPTION

This class uses BioFetch protocol based service to retrieve Medline references by their ID.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org              - General discussion
  http://bioperl.org/MailList.shtml  - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via email or the web:

  bioperl-bugs@bioperl.org
  http://bioperl.org/bioperl-bugs/

AUTHOR

Heikki Lehvaslaiho (heikki@ebi.ac.uk)

COPYRIGHT

Copyright (c) 2002 European Bioinformatics Institute. All Rights Reserved.

This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

DISCLAIMER

This software is provided "as is" without warranty of any kind.

BUGS AND LIMITATIONS

  • Only method get_by_id() is supported.

APPENDIX

The main documentation details are to be found in Bio::DB::BiblioI.

Here is the rest of the object methods. Internal methods are preceded with an underscore _.

get_by_id

 Title   : get_by_id
 Usage   : $entry = $db->get__by_id('20063307')
 Function: Gets a Bio::Biblio::RefI object by its name
 Returns : a Bio::Biblio::Medline object
 Args    : the id (as a string) of the reference

get_all

  Title   : get_all
  Usage   : $seq = $db->get_all($ref);
  Function: Retrieves reference objects from the server 'en masse', 
            rather than one  at a time.  For large numbers of sequences, 
            this is far superior than get_by_id().
  Example :
  Returns : a stream of Bio::Biblio::Medline objects
  Args    : $ref : either an array reference, a filename, or a filehandle
            from which to get the list of unique ids/accession numbers.

get_seq_stream

 Title   : get_seq_stream
 Usage   : my $seqio = $self->get_seq_sream(%qualifiers)
 Function: builds a url and queries a web db
 Returns : a Bio::SeqIO stream capable of producing sequence
 Args    : %qualifiers = a hash qualifiers that the implementing class 
           will process to make a url suitable for web querying 

postprocess_data

 Title   : postprocess_data
 Usage   : $self->postprocess_data ( 'type' => 'string',
                                     'location' => \$datastr);
 Function: process downloaded data before loading into a Bio::SeqIO
 Returns : void
 Args    : hash with two keys - 'type' can be 'string' or 'file'
                              - 'location' either file location or string 
                                           reference containing data

VERSION and Revision

 Usage   : print $Bio::DB::Biblio::biofetch::VERSION;
           print $Bio::DB::Biblio::biofetch::Revision;

Defaults

 Usage   : print $Bio::DB::Biblio::biofetch::DEFAULT_SERVICE;